2X18 | pdb_00002x18

The crystal structure of the PH domain of human AKT3 protein kinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UNP	PDB ENTRY 1UNP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2M PROLINE, 0.1M HEPES PH 7.5, 10% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.475	α = 111.47
b = 62.401	β = 102.75
c = 71.411	γ = 94.36

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD		2009-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.46	64.03	98.1	0.08	10	3.5		164858			15.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.54	94.3		0.47	2	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UNP	1.46	64.03	156074	8269	98.11	0.19156	0.18934	0.2	0.23377	0.24	RANDOM	10.825

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.11	-0.22	-0.22	-0.35	0.01	0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.622
r_dihedral_angle_4_deg	13.965
r_dihedral_angle_3_deg	13.619
r_scangle_it	8.652
r_dihedral_angle_1_deg	6.36
r_scbond_it	6.19
r_mcangle_it	3.835
r_mcbond_it	2.557
r_angle_other_deg	2.369
r_angle_refined_deg	1.658
r_mcbond_other	0.83
r_chiral_restr	0.119
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7506
Nucleic Acid Atoms
Solvent Atoms	1717
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing